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gnu: Add trust4.

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gnu/packages/bioinformatics.scm (trust4): New variable.

Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
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Mădălin Ionel Patrașcu 2024-02-23 10:11:49 +01:00 committed by Ricardo Wurmus
parent 57769fb0b3
commit 709e87caff
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@ -5930,6 +5930,82 @@ be of arbitrary length. Repeats with pattern size in the range from 1 to 2000
bases are detected.")
(license license:osl2.1)))
(define-public trust4
(package
(name "trust4")
(version "1.0.13")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/liulab-dfci/TRUST4")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "058wd5bklgcsb0r8l7n1ffakbj4c3ac5hjyvmaqhr3p233fl44z7"))
(modules '((guix build utils)))
(snippet '(begin
;; Remove bundled samtools
(delete-file-recursively "samtools-0.1.19")))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #f ;there are no tests
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'use-samtools-headers
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "Makefile"
(("LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19")
(string-append "LINKPATH= -I."
#$(this-package-native-input "samtools")
"/include/samtools"
" -L."
#$(this-package-native-input "samtools")
"/lib"))
(("./samtools-0.1.19/")
(string-append #$(this-package-native-input
"samtools") "/lib/")))
(substitute* "alignments.hpp"
(("samtools-0.1.19")
(string-append #$(this-package-native-input
"samtools") "/include/samtools")))))
(delete 'configure) ; No configure.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
(scripts (string-append #$output
"/share/trust4/scripts")))
(install-file "annotator" bin)
(install-file "bam-extractor" bin)
(install-file "fastq-extractor" bin)
(install-file "run-trust4" bin)
(install-file "trust4" bin)
;; install scripts stored in the scrips dir
(for-each (lambda (file)
(chmod file #o555))
(find-files "scripts" "\\.p(y|l)"))
(copy-recursively "scripts" scripts)
(delete-file-recursively "scripts")
;; install the rest of the scripts that are in the main dir
(for-each (lambda (file)
(chmod file #o555)
(install-file file bin))
(find-files "." "\\.(pl|py|sh)"))))))))
(native-inputs (list automake samtools-0.1))
(inputs (list perl python-wrapper zlib))
(home-page "https://github.com/liulab-dfci/TRUST4")
(synopsis "TCR and BCR assembly from RNA-seq data")
(description "This package is analyzing @acronym{TCR, T cell receptor} and
@acronym{BCR, B cell receptor} sequences using unselected RNA sequencing data,
profiled from fluid and solid tissues, including tumors. TRUST4 performs de
novo assembly on V, J, C genes including the hypervariable @acronym{CDR3,
complementarity-determining region 3} and reports consensus contigs of BCR/TCR
sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to
identify the corresponding gene and CDR3 details. TRUST4 supports both single-end
and paired-end bulk or single-cell sequencing data with any read length.")
(license license:gpl3)))
(define-public diamond
(package
(name "diamond")